\

Search for Variation information by Variation ID:

Please input a variation ID (e.g., vg0722097923 , STR0500036000 ).

Detailed information for vg0316518526:

Variant ID: vg0316518526 (JBrowse)Variation Type: SNP
Chromosome: chr03Position: 16518526
Reference Allele: TAlternative Allele: C
Primary Allele: CSecondary Allele: T

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.97, T: 0.03, others allele: 0.00, population size: 250. )

Flanking Sequence (100 bp) in Reference Genome:


GCCACGCGATCGAAGACGATCTACATGCGTTAACACAAAATCCGGGCGAATCCTTGAGGGACTATGTATGACGCTTTAATGAGTGTAGAAATACAATCCC[T/C]
GAAATCACCGACGCCTCTGTGATTCGCGCTTTCAAAATCGGTGTCAGAGATCGCTATACTACCCAGGAGTTGGCAACAAGTCGAATCACAACTACTCGAA

Reverse complement sequence

TTCGAGTAGTTGTGATTCGACTTGTTGCCAACTCCTGGGTAGTATAGCGATCTCTGACACCGATTTTGAAAGCGCGAATCACAGAGGCGTCGGTGATTTC[A/G]
GGGATTGTATTTCTACACTCATTAAAGCGTCATACATAGTCCCTCAAGGATTCGCCCGGATTTTGTGTTAACGCATGTAGATCGTCTTCGATCGCGTGGC

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of T(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 62.70% 24.10% 0.66% 12.59% NA
All Indica  2759 79.20% 15.50% 0.18% 5.11% NA
All Japonica  1512 33.20% 39.90% 1.52% 25.33% NA
Aus  269 76.60% 1.50% 0.74% 21.19% NA
Indica I  595 62.40% 37.60% 0.00% 0.00% NA
Indica II  465 92.30% 5.60% 0.43% 1.72% NA
Indica III  913 84.20% 8.50% 0.00% 7.23% NA
Indica Intermediate  786 78.40% 12.70% 0.38% 8.52% NA
Temperate Japonica  767 7.30% 50.50% 2.35% 39.90% NA
Tropical Japonica  504 66.30% 25.60% 0.40% 7.74% NA
Japonica Intermediate  241 46.50% 36.50% 1.24% 15.77% NA
VI/Aromatic  96 12.50% 83.30% 0.00% 4.17% NA
Intermediate  90 64.40% 23.30% 1.11% 11.11% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0316518526 T -> C LOC_Os03g29075.1 synonymous_variant ; p.Pro547Pro; LOW synonymous_codon Average:57.187; most accessible tissue: Minghui63 young leaf, score: 71.839 N N N N
vg0316518526 T -> DEL LOC_Os03g29075.1 N frameshift_variant Average:57.187; most accessible tissue: Minghui63 young leaf, score: 71.839 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0316518526 NA 2.02E-06 mr1542 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0316518526 NA 1.91E-07 mr1456_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0316518526 NA 9.90E-08 mr1542_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0316518526 8.74E-06 8.74E-06 mr1547_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0316518526 NA 4.06E-09 mr1624_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0316518526 6.01E-06 6.01E-06 mr1719_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0316518526 NA 2.82E-06 mr1740_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0316518526 3.90E-06 1.01E-08 mr1780_2 Jap_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0316518526 NA 7.19E-06 mr1844_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0316518526 6.82E-06 6.82E-06 mr1895_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0316518526 4.23E-06 4.23E-06 mr1914_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0316518526 2.49E-06 2.49E-06 mr1981_2 Jap_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251